Removing index.php from Code Igniter - php

Question

I've done a search for my question but have yet seen one similar to mine.
I have a newly installed CI on my server, for security reason I have shifted the "application" and "system" folder outside of public_html and into a folder called "app". I tried a lot of methods that the forums were using but none seem to help.
Below is my folder structure, would like to know what to type for the .htaccess and where does this .htaccess go to?
/
app (system and application folder for CI resides here)
public_html (index.php - the one which defines ENVIRONMENT, styles, other htmls and my current .htaccess resides here)
My current .htaccess looks like this:
RewriteEngine on
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule .* index.php/$1 [PT,L]
Please help! Thank you for your time!
EDIT
Currently my url is something like this
xxx.xxx.xxx.xxx/~app/index.php/user/check/id
(it's on a shared hosting but not linked to domain yet and hence the ip address and partition in the url.)
I want to achieve something like
xxx.xxx.xxx.xxx/~app/user/check/id
and it should work when I link up my domain. (e.g. www.mydomain.com/user/check/id)

Answer 1

Alright, I think I've solved the problem.
This has most probably got to do with the 'unique' url that I have. I assume if it is a normal domain name it shouldn't have so much problems.
My url > xxx.xxx.xxx.xxx/~app/index.php/user/check/id
My directory structure remains the same >
/app (application and system directories goes here)
/public_html (index.php and .htaccess goes here)
.htaccess code as follows:
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /~app/ << NOTE the addition
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php/$1 [L]
</IfModule>
In config.php, set
$config['base_url'] = 'http://xxx.xxx.xxx.xxx/~app/';
$config['index_page'] = '';
That's all!